|
| Status |
Public on Sep 07, 2012 |
| Title |
pbMEC_S. aureus_1h_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
pbMEC callenged with S. aureus for 1h
|
| Organism |
Bos taurus |
| Characteristics |
cell type: primary bovine mammary epithelial cells
treatment: heat inactivated S. aureus
time: 1 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was linearly amplified with T7-RNA polymerase in an in vitro transcription (IVT) reaction, and labeled with biotinylated ribonucleotides (GeneChip® IVT Labeling Kit, Affymetrix)
|
| |
|
| Hybridization protocol |
10 µg of biotin labelled, purified and fragmented cRNA was then hybridized onto GeneChip® Bovine Genome Arrays (Affymetrix) during a 16-hour incubation at 45°C. Posthybridization staining and washing was performed using an automated protocol on the Fluidics Station 450 (Affymetrix)
|
| Scan protocol |
Arrays were scanned with a GeneChip® scanner 3000 7G
|
| Description |
Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of S. aureus strain 1027 for 1h
|
| Data processing |
Background correction, normalization and summation was performed using GCRMA. Only such genes were further processed exhibiting at least three present-calls. The gene expression values for the various points in time were estimated with a linear model. In order to account for multiple testing, the false discovery rate approach was used and we selected only the genes with a q-value ≤ 0.05. In a further filtering step, only genes with a fold-change ≥ 2 in the time profile were kept.
|
| |
|
| Submission date |
Nov 16, 2010 |
| Last update date |
Sep 07, 2012 |
| Contact name |
Juliane Guenther |
| E-mail(s) |
[email protected]
|
| Organization name |
Leibniz-Institute for Farm Animal Biology (FBN)
|
| Street address |
Wilhelm-Stahl-Allee 2
|
| City |
Dummerstorf |
| ZIP/Postal code |
D-18196 |
| Country |
Germany |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE25413 |
Expression data from primary bovine mammary epithelial cells (pbMEC) challenged with heat inactivated E. coli and S. aureus particles |
|
